Various devices incorporate optical or opto-electronic modules. Such modules are sometimes manufactured at the wafer level to facilitate the fabrication of multiple modules at the same time. Fabrication of the modules sometimes includes stacking multiple wafers one atop the other, where each wafer provides some particular functionality for the resulting modules. One or more of the wafers, which can be referred to as an optics wafer, may incorporate various optical elements. Although fabricating the modules at the wafer level can facilitate the overall manufacturing process, variations across the wafer can present challenges in such fabrication processes.